Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health)

Statistical Methods in Bioinformatics: An Introduction (Statistics for Biology and Health)

Advances in computers and biotechnology have had an immense impact on the biomedical fields, with broad consequences for humanity. Correspondingly, new areas of probability and statistics are being developed specifically to meet the needs of this area. There is now a necessity for a text that introduces probability and statistics in the bioinformatics context. This book also describes some of the main statistical applications in the field, including BLAST, gene finding, and evolutionary inference, much of which has not yet been summarized in an introductory textbook format. This book grew out of a need to teach bioinformatics to graduate students at the University of Pennsylvania. At the same time however, it is organized to appeal to a wider audience. In particular it should appeal to any biologist or computer scientist who wants to know more about the statistical methods of the field, as well as to a trained statistician who wishes to become involved in bioinformatics. The earlier chapters introduce the concepts of probability and statistics at an elementary level, and will be accessible to students who have only had introductory calculus and linear algebra. Later chapters are immediately accessible to the trained statistician. Only a basic understanding of biological concepts is assumed, and all concepts are explained when used or can be understood from the context. Several chapters contain material independent of that in other chapters, so that the reader interested in certain areas can proceed directly to those areas. Warren Ewens is Professor of Biology at the University of Pennsylvania. He is the author of two books, Population Genetics and Mathematical Population Genetics, and has served on the editorial boards of Theoretical Population Biology, GENETICS, Proceeding of the Royal Society B and SIAM Journal in Mathematical Biology. He was recently awarded the Gold Medal of the Australian Statistical Society and elected as Fellow of the Royal Society. His research interests are in evolutionary population genetics, linkage analysis for human diseases, and bioinformatics. Gregory Grant is a bioinformatics researcher at the University of Pennsylvania in the Computational Biology and Informatics Laboratory (CBIL), where he has been since 1998. In 1995 he received a Ph.D. in Mathematics from the University of Maryland and in 1999 a Masters in Computer Science from the University of Pennsylvania. His research interests are in bioinformatics in general and in particular in the statistical analysis of gene expression data and significance testing methods for IBD-mapping.

Rating: (out of 4 reviews)

List Price: $ 115.00

Price: $ 57.43

Statistical Analysis of Network Data: Methods and Models (Springer Series in Statistics)

In the past decade, the study of networks has increased dramatically. Researchers from across the sciences—including biology and bioinformatics, computer science, economics, engineering, mathematics, physics, sociology, and statistics—are more and more involved with the collection and statistical analysis of network-indexed data. As a result, statistical methods and models are being developed in this area at a furious pace, with contributions coming from a wide spectrum of disciplines.

This book provides an up-to-date treatment of the foundations common to the statistical analysis of network data across the disciplines. The material is organized according to a statistical taxonomy, although the presentation entails a conscious balance of concepts versus mathematics. In addition, the examples—including extended cases studies—are drawn widely from the literature. This book should be of substantial interest both to statisticians and to anyone else working in the area of ‘network science.’

The coverage of topics in this book is broad, but unfolds in a systematic manner, moving from descriptive (or exploratory) methods, to sampling, to modeling and inference. Specific topics include network mapping, characterization of network structure, network sampling, and the modeling, inference, and prediction of networks, network processes, and network flows. This book is the first such resource to present material on all of these core topics in one place.

List Price: $ 89.95

Price: $ 71.93

Probabilistic analysis of gene expression measurements from heterogeneous tissues

Motivation: Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in experiments that focus on studying cell types, e.g. their expression profiles, in isolation. Although sample heterogeneity can be addressed by manual microdissection, prior to conducting experiments, computational treatment on heterogeneous measurements have become a reliable alternative to perform this microdissection in silico. Favoring computation over manual purification has its advantages, such as time consumption, measuring responses of multiple cell types simultaneously, keeping samples intact of external perturbations and unaltered yield of molecular content.

Results: We formalize a probabilistic model, DSection, and show with simulations as well as with real microarray data that DSection attains increased modeling accuracy in terms of (i) estimating cell-type proportions of heterogeneous tissue samples, (ii) estimating replication variance and (iii) identifying differential expression across cell types under various experimental conditions. As our reference we use the corresponding linear regression model, which mirrors the performance of the majority of current non-probabilistic modeling approaches.

Availability and Software: All codes are written in Matlab, and are freely available upon request as well as at the project web page http://www.cs.tut.fi/~erkkila2/. Furthermore, a web-application for DSection exists at http://informatics.systemsbiology.net/DSection.

Bioinformatics – recent issues

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)

This introductory text offers a clear exposition of the algorithmic principles driving advances in bioinformatics. Accessible to students in both biology and computer science, it strikes a unique balance between rigorous mathematics and practical techniques, emphasizing the ideas underlying algorithms rather than offering a collection of apparently unrelated problems.

The book introduces biological and algorithmic ideas together, linking issues in computer science to biology and thus capturing the interest of students in both subjects. It demonstrates that relatively few design techniques can be used to solve a large number of practical problems in biology, and presents this material intuitively.

An Introduction to Bioinformatics Algorithms is one of the first books on bioinformatics that can be used by students at an undergraduate level. It includes a dual table of contents, organized by algorithmic idea and biological idea; discussions of biologically relevant problems, including a detailed problem formulation and one or more solutions for each; and brief biographical sketches of leading figures in the field. These interesting vignettes offer students a glimpse of the inspirations and motivations for real work in bioinformatics, making the concepts presented in the text more concrete and the techniques more approachable.

PowerPoint presentations, practical bioinformatics problems, sample code, diagrams, demonstrations, and other materials can be found at the Authors’ website.

Rating: (out of 9 reviews)

List Price: $ 63.00

Price: $ 35.99

Transactions on Computational Biology & Bioinformatics

Transactions on Computational Biology & Bioinformatics

Transactions on Computational Biology and Bioinformatics publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology; the development and testing of effective computer programs in bioinformatics; the development and optimization of biological databases; and important biological results that are obtained from the use of these methods, programs, and databases.

Rating: (out of 1 reviews)

Price: $ 425.00

More Products

PatternBranching/ProfileBranching – Finding subtle motifs by branching from sample strings

Finding subtle motifs by branching from sample strings. Price A., Ramabhadran S., Pevzner P.A. 2003. To appear in Bioinformatics supplementary edition, Proceedings of the Second European Conference on Computational Biology (ECCB-2003). Paris, France.

Abstract:
Many motif finding algorithms apply local search techniques to a set of seeds. For example, GibbsDNA (Lawrence et al., 1993) applies Gibbs sampling to random seeds, and MEME (Bailey and Elkan, 1994) applies the EM algorithm to sample strings, i.e. substrings of the sample. In the case of subtle motifs, recent benchmarking efforts show that both random seeds and selected sample strings may never get close to the globally optimal motif. We propose a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings. Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms.

Download source

« Previous Page — Next Page »